From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species.

ABSTRACT:

Background

Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome seq

SUBMITTER: Wright B 

PROVIDER: S-EPMC6547446 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature